Data download links
To download user must provide details as follows: User id: reggen and password unipath@123
We have included precompiled pathway scores for few scATAC-seq studies using pathway annotation file having 1329 pathways which can be downloaded from the link:Precompiled pathway scores for various studies using two pathway annotation files for scRNAseq data can be downloaded from the link:
Precompiled cell detection scores for various scRNAseq data can be downloaded from the link:
Mandatory files required for conversion of scATAC-seq profiles to pathway scores can be downloaded from the link:
Additional files:
We have included tSNE coordinates for study id: GSE108097 (Single cell mouse altas dataset) in the link:
We have included codes and datasets used in the paper to replicate the results and figures in the following links:
Codes for Figure 1
Codes and datasets used for comparison of UniPath in terms of cell type detection with AUCell,GSVA and PAGODA for Figure 1A can be found in the link:
Codes and datasets used to evaluate consistency of UniPath to give correct pathways and its comaprison with AUCell,GSVA and PAGODA for Figure 1B can be found in the link:
Code and dataset used for creating barplots for Figure 1D can be found in the link:
Precompiled pathway scores and code for Figure 1E can be found in the link:
Codes for Figure 2
For Figure 2A, code and data can be accessed from the link:
We have included codes and datasets used for evaluating performance of UniPath with AUCell, GSVA and PAGODA in terms of visualization and clustering for the Figure 2B and supplementary Figure S8 in the link:
For replicating results from the Figure 2C codes and datasets can be found in the link:
Codes for Figure 3
Codes and datasets used for running Monocle, TSCAN, cellTree and Diffusion Maps for the Figure 3A can be found in the link:
Code for pseudo temporal ordering used in case of UniPath for the Figure 3B can be found in the link:
Code used in Figure 3C can be found in the link:
Code and data used for replicating Figure 3D can be found in the link. This link contains three codes correponding to three figures along with a readme.txt file:
Codes for Figure 4
User can use tsne coordinates directly or precompiled pathway scores for Figure 4A from the link:
Code and datasets used in Figure 4C can be found in the link:
Codes for Figure 5
Code used for the Figure 5A can be found in the link:
Code used for Figure 5B can be found in the link:
Code and dataset used for plotting heatmaps of correlation of pathways in Figure 5C can be found in the link:
Code and dataset used for getting correlation values in Figure 5D can be found in the link:
Code and dataset used for replicating results in Figure 5E can be found in the link: